Recent biochemical and genetic evidence provides strong support that obesity and related metabolic disorders develop from defects in mitochondrial function. These defects produce excess cellular oxidative stress mediated by reactive oxygen species (ROS). One mechanism that appears to improve outcomes in metabolic disorders is mitochondrial proton leak, i.e., the uncoupling of energy production from respiration in the mitochondria. Mild uncoupling in mitochondrial respiration mediated by uncoupling proteins (UCPs) has been reported to decrease fat storage and ROS production in animals and favorably modifies insulin sensitivity. Using 18 unrelated wild-type inbred lines of D. melanogaster, we have shown that naturally occurring genetic variation affects inter-individual variability in mitochondrial state 4 respiration rates (e.g. basal proton leak) in skeletal muscles. We have also shown that variation in mitochondrial state 4 respiration rates in skeletal muscles is negatively correlated with variation in fat storage. This implies that some genotypes have higher mitochondrial coupling efficiency and store higher quantities of fat while other genotypes have lower coupling efficiency and require more energy for maintaining their mitochondrial electrochemical gradient. These observations raise the important question of why variation in mitochondrial proton leak (e.g. metabolic inefficiency) is evolutionary conserved in natural populations. We speculate that the trade-off between mitochondrial state 4 respiration and fat storage observed in our preliminary studies is a reflection of the allocation of finite resources between competing organismal functions. Our hypothesis is that while individuals with efficient mitochondrial coupling can successfully use their fat storage for reproduction and for coping with environmental challenges, such as fighting infection, those with less coupling efficiency will need to use more energy for maintaining their mitochondrial electrochemical gradient at the expense of other organismal functions. However, mitochondrial basal proton leak may decrease ROS generation and, therefore, protect against cellular degeneration and aging. The Specific Aims of this project are to: (1) Perform a genome-wide association scan to map genetic variants affecting naturally occurring variation in muscle-specific mitochondrial bioenergetics, ROS production, energy metabolism traits, food intake, innate immune response, and female fecundity. (2) Determine the gene co-expression network regulating mitochondrial bioenergetic traits in young flies (3-5 days old). (3) Verify whether 10 of the hub genes identified by the analyses performed in Aim 2 are responsible for the coordinated regulation of mitochondrial bioenergetics and also impact whole-organism energy homeostasis and life-history traits. (4) Investigate whether genetic variants in human orthologs of the 10 Drosophila candidate genes identified in the previous aims are associated with phenotypic variation in human obesity and related metabolic outcomes. These studies will provide new insights into the genetic basis of mitochondrial coupling efficiency as it relates to metabolic, immune response and life-history traits.